Greater efforts to provide alternative scenarios are key to successful urban stream restoration planning. In this study, we discuss two different aspects of water quality management schemes, biodegradation and human health, which are incorporated in the restoration project of original, pristine condition of urban stream at the Gwangju (GJ) Stream, Korea. For this study, monthly monitoring of biochemical oxygen demand (BOD5) and fecal indicator bacteria (FIB) data were obtained from 2003 to 2008 and for 2008, respectively, and these were evaluated to explore pollutant magnitude and variation with respect to space and time window. Ideal scenarios to reduce target pollutants were determined based on their seasonal characteristics and correlations between the concentrations at a water intake and discharge point, where we suggested an increase of environmental flow and wetland as pollutants reduction drawing for BOD5 and FIB, respectively. The scenarios were separately examined by the Qual2E model and hypothetically (but planned) constructed wetland, respectively. The results revealed that while controlling of the water quality at the intake point guaranteed the lower pollution level of BOD5 in the GJ Stream, a wetland constructed at the discharge point may be a promising strategy to mitigate mass loads of FIB. Overall, this study suggests that a combination of the two can be plausible scenarios not only to support sustainable urban water resources management, but to enhance a quality of urban stream restoration assignment.